Biological Dynamics & Networks
CHE 559 / PHY 559 / AMS 537
Spring Tu/Th 2:303:50 pm in Laufer Center 101
Tom MacCarthy, Course PI
Guest lecturers: Ken Dill, TBA
This course will provide a solid foundation in key theoretical concepts for the study of dynamics in biological systems and networks at different scales ranging from the molecular level to metabolic and gene regulatory networks.
Reference Books
 Ken Dill, Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience
 Bernhard Palsson, Systems Biology: simulation of dynamic network states
 Eberhard Voit, A first course in Systems Biology
 Uri Alon, An introduction to Systems Biology
 M.E.J. Newman, Networks: an introduction
Topics  Speakers 

Introduction to networks and statistical thermodynamics

MacCarthy, Dill 
Statistical thermodynamics II

Dill 
Biochemical networks
Reference: Palsson, Chapters 2 and 4 
MacCarthy 
Enzyme kinetics
Reference: Palsson, Chapter 5 
MacCarthy 
Network measurements
Reference: Newman, Chapters 6,7 
MacCarthy 
Largescale structure of networks
Reference: Newman chapter 8 
TBA 
Network evolution models
Reference: Newman chapters 12,14 
TBA 
Metabolic networks I
Reference: Palsson, Chapters 7 and 10 
MacCarthy 
Metabolic networks II
Reference: Voit, Chapters 3 and 8 
MacCarthy 
Gene regulatory networks I
Reference: Alon, Chapters 24 
MacCarthy 
Signal transduction systems
Reference: Voit, Chapter 9 
MacCarthy 
Robustness
Reference: Alon, Chapters 7,8 
MacCarthy 
Algorithms for network analysis
Reference: Newman, Chapter 11 
MacCarthy 
Modeling noise

TBA 